(1) Very little attention seems to have been given to the problem of how to peel back the masquerade without various major world governments trying to make vampires extinct. I infer that this will be the primary conflict of book 3.

(2) What is the best choice of long-term dominant species? The known species so far are vampires, half-vampires, possibly other fractions of vampire, werewolves, and non-wolf humans (let's call them muggles).

Muggles have the major disadvantage of being mortal. Werewolves can't reproduce without help from muggles or half-vampires. Male half-vampires may or may not be able to reproduce at all, as there appear to be several sex-linked issues relating to half-vampires, such as vampire fertility and half-vampire venom.

Vampires have three different Chelsea-level-creepy major psychological changes: the Thirst for human blood, the mate Bond, and the Freeze in personality and personal development. Male werewolves likewise suffer from imprinting.

Creating a population that can never reproduce, such as everyone being a vampire with no muggles left, pretty much guarantees extinction eventually. The average vampire lifespan is probably well under ten thousand years. Even if the Golden Empire somehow manages to improve that by, say, a factor of a million, we still have a finite expected-time-to-live for People In General.

An all-werewolf-and-vampire population might or might not be able to reproduce, if the females never activated and were turned after menopause.

If half-vampires can mate with each other to produce more half-vampires, then they would seem to be the best choice. Unfortunately, the half-vampire population is at present critically low. Perhaps, as the unmasqueing starts to bottleneck, preference should be given to women who are willing to carry a half-vampire child to term before turning.

There will be no Book 3. There will be some short stories (see the announcement I just posted) but I'm planning for at least most of them to take place in "the past".

Male half-vampires can reproduce, with half-vampires or "muggles" or with mostly-muggle hybrids.

Werewolves can reproduce without help (although they will not activate without any vampires present). A female werewolf who quits her wolf amounts to a physically-25-year-old "muggle" who will pass on wolfiness to all of her children, and male wolves are obviously capable of siring children with "muggles", presumed capable of doing so with half-vampires, and demonstrably capable of doing so with non-active wolves. (Two of the currently-active wolves have a child together from before they activated.)

There is no particular reason why a population consisting entirely, or almost entirely, of half-vampires or other degrees of hybrid-ness wouldn't work.

No. An active female werewolf cannot get pregnant. Sustaining an all-wolf population, however, is possible without people dying of old age if one waits to activate the females until after they have had however many kids; they retain the ability to activate until age 25.